Notes on DNA Replication

Overview of DNA Replication

• Semi-conservative: Each new DNA molecule consists of one old strand (red) and one new strand (blue).
• Anti-parallel strands: One strand runs 5' to 3' and the other 3' to 5'.
• Complementary base pairing:
  • A pairs with T (2 hydrogen bonds)
  • G pairs with C (3 hydrogen bonds)

Key Concepts

DNA Structure

• Base Pairing: Given the sequence of one strand, the other can be predicted. For example,
  • Original Strand: A, T, T, G, A, T, C
  • Complementary Strand: T, A, A, C, T, A, G

Hydrogen Bonds

• Bonds between nucleotides:
  • A-T: 2 hydrogen bonds
  • G-C: 3 hydrogen bonds

DNA Replication Process

Directionality

• Bidirectional Replication:
  • DNA replication proceeds in two directions from the origin of replication.
• Unidirectional Replication:
  • Synthesis occurs in one direction only.

Enzymes Involved

• Helicase: Unwinds DNA by breaking hydrogen bonds.
• DNA Gyrase: A topoisomerase that relieves torsional strain ahead of the replication fork.
• Single-Stranded Binding Proteins (SSB): Stabilize and protect separated strands.
• Primase: Synthesizes RNA primer needed for DNA replication initiation.
• DNA Polymerase III: Synthesizes new DNA strands in the 5' to 3' direction.
• DNA Polymerase I: Replaces RNA primer with DNA.
• DNA Ligase: Seals nicks between Okazaki fragments.

Types of Strands

• Leading Strand: Synthesized continuously in the same direction as the replication fork (5' to 3').
• Lagging Strand: Synthesized discontinuously in the opposite direction (produces Okazaki fragments).
  • Semi-discontinuous: Continuous on the leading strand; discontinuous on the lagging strand.

Proofreading Mechanisms

• Exonuclease Activity:
  • DNA Polymerase III: 3' to 5' exonuclease activity for proofreading.
  • DNA Polymerase I: 5' to 3' exonuclease activity for DNA repair.

Summary of Enzymes and Their Functions

• Helicase: Separates DNA strands.
• Topoisomerase (DNA Gyrase): Reduces torsional strain.
• SSB Proteins: Stabilize single-stranded DNA.
• Primase: Creates RNA primer.
• DNA Polymerase III: Synthesizes new DNA in the 5' to 3' direction.
• DNA Polymerase I: Replaces RNA primers with DNA.
• DNA Ligase: Joins Okazaki fragments.

Practice Problems Review

• True Statements:
  • DNA replication is semi-conservative.
  • Helicase separates the DNA strands.
  • DNA strands are complementary and anti-parallel.
• False Statements:
  • DNA replication is continuous (it is semi-discontinuous).
  • DNA Polymerase III does not have 5' to 3' exonuclease activity (only DNA Polymerase I does).

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• Review key concepts and enzyme functions to prepare for quizzes and exams.
• Understand the differences between leading and lagging strands.